Systems Ecology of Microbiomes: Function Is Key

Abstract

Microbiomes represent highly dynamic and heterogeneous systems, which
exhibit tremendous complexity at all levels. High-throughput molecular
measurements are allowing unprecedented insights into microbiome composition,
physiology, ecology and evolution in situ. Our group has pioneered a
comprehensive toolbox comprising wet- and dry-lab methodologies to enable
systematic measurements of microbiomes over space and time, the integration and
analysis of the resulting multi-omic data, and experimental models for rapidly
testing hypotheses in vitro. The application of these methods has
culminated in essential new insights regarding niche ecology and resulting
lifestyle strategies of specific microbial populations in situ as well
as the discovery of keystone functional genes. In the context of the human gut
microbiome, it has highlighted the disruption of ecosystem services in the
context of human disease (type 1 diabetes). To study the ramifications of such
perturbations, a microfluidics-based model of the gastrointestinal
human-microbe interface has been developed called HuMiX. HuMiX allows the
probing of the molecular interactions between human and microbial cell
contingents and has highlighted the importance of microbial metabolism in
governing human cell physiology in the gut. The developed toolbox is also
particularly pertinent for the exploration of the vast expanse of unknown
features in microbiomes, ranging from uncharacterised organisms to proteins of
unknown function and small molecules. Thereby, Microbial Systems Ecology offers
great potential for the discovery of new biological functions in the future.